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Epstein-Barr Virus and Methylation Patterns

Christopher Oakes from The Ohio State University spoke at London Calling 2019 on “Discerning the origin of Epstein-Barr virus in patients using nanopore-derived DNA methylation signatures.” Oakes spoke about how they study tumor viruses and cancer. The Epstein-Barr virus is common, the “prototypical cancer virus,” according to Oakes. Immune cells suppress the virus, but the […]
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Determining Breakpoints and Duplications during Genetic Testing

Chris T.L. Chan from the Hong Kong Sanitorium & Hospital in China spoke at London Calling 2019 on “Long-read NGS guided preimplantation genetic testing for chromosomal structural rearrangement.” Chan presented a clinical scenario. They explained that short-read sequencing allowed the analysis of copy number variation from blood samples. Loss of copy can be identified with […]
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Identification of Retrotransposons in Cancer and Germline Samples

Tonight, I watched Kimmo Palin from the University of Helsinki present at London Calling 2019 on “Retrotransposon variation in human genome and tumorigenesis.” They began by discussing retrotransposons and describing them as “copy-paste elements” in the genome that copy themselves with an RNA intermediate. They range in size between 300 bp and 6,000 bp. LINE1 […]
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Complex Karyotype Analysis with Nanopore Sequencing

Anna Dolnik from the Charite University Medical Center in Berlin, Germany, presented at London Calling 2019 on “Genomic profiling in acute myeloid leukemia with complex karyotype.” They presented data on the survival of over 5,100 patients with acute myeloid leukemia (AML). The WHO in 2016 revised the classification of AML. A newly diagnosed AML patient, […]
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Long-read Human Genome Sequencing Service

Andrea Riposati from Dante Labs in the US presented at London Calling 2019 on “Human long-read whole genome sequencing: applications and results.” Riposati is the co-founder and CEO of Dante Labs. They presented a case of a patient who had suffered 45 years without a diagnosis. Dante Labs provided whole genome sequencing and pharmacogenomics lab. […]
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The Mobile Suitcase Lab in Action

Tonight I watched the London Calling 2019 session by Ahmed Abd El Wahed from the University of Gottingen in Germany. The title of the presentation was “From ancient tomb to animal viruses: mobile suitcase lab for nanopore sequencing at field settings.” El Wahed spoke about the reagents and equipment needed to perform sequencing. They have […]
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Splicing Detection with Long Reads

Kuan-Ting Li from Cold Spring Harbor Laboratory presented at London Calling 2019 on “PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis.” PSI-Sigma is a splicing detection tool that measures percent spliced in. With nanopore long-read RNA-seq data, PSI sigma presents a newer splicing detection approach. PSI-sigma was benchmarked on synthetic RNAs and […]
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Replication Fork Mapping in Eukaryotes

Magali Hennion from the Institute of Biology of the Ecole Normale Superieure in France presented at London Calling 2019 on “Mapping DNA replication using nanopore sequencing.” DNA replication in eukaryotes starts from multiple origins, and the fork progresses with variable speeds. Hennion explained that replication is important in understanding tumorigenesis. Single-molecule approaches are needed to […]
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Repeat Expansion Analysis

Pay Giesselmann from the Max Planck Institute for Molecular Genetics in Germany presented at London Calling 2019 on “Nanopype: processing and quantification of short tandem repeats.” The team created a data processing pipeline for targeted repeat expansion analysis and worked on STRique to quantify repeat expansion. Nanopype can be installed from the source, used as […]
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